knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
knitr::opts_chunk$set(echo = F, warning = F, message = F)

seu_merge_epi_p007n_epi_p007t_epi_p008n_epi_p008t_epi_p009n1_epi_p009n2_epi_p009t1_epi_p009t2_epi_p012n_epi_p012t_epi_p013n_epi_p013t_epi_p014n_epi_p014t_epi_p016n_epi_p016t_epi_p017n_epi_p017t.rds

Signature scoring

##  [1] "p007n"  "p007t"  "p008n"  "p008t"  "p009n1" "p009n2" "p009t1"
##  [8] "p009t2" "p012n"  "p012t"  "p013n"  "p013t"  "p014n"  "p014t" 
## [15] "p016n"  "p016t"  "p017n"  "p017t" 
## [1] "broad done"
## [1] "morkel done"
## [1] "SMAD done"
## [1] "TNFa done"
## [1] "Wnt done"
## [1] "YAP done"
## [1] "regev done"

Louvain clusters

Cluster marker genes

rank 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
1 CA1 AQP8 HEXIM1 CLCA1 RPS6 RPS7 RNF43 ZG16 MMP7 SH2D6 TFF3 SPINK4 PLA2G2A MT-CO3 GUCA2B HMGB1 CLCA4 XIST TSHZ2 REG1A SPP1
2 FABP1 CLCA4 SOX4 FCGBP RPS3A RPL21 GAS6-AS1 MUC2 S100A11 LRMP SPINK4 CLCA1 OLFM4 MT-CO2 CA7 HSPD1 AQP8 MT-CO2 SLC7A11 REG1B CXCR4
3 PHGR1 SLC26A3 HES1 ITLN1 RARRES2 RPS4X DPEP1 TFF1 PERP TRPM5 ITLN1 ITLN1 PIGR CA1 OTOP2 RPL21 SLC26A3 MT-CO3 FTL KRT23 VIM
4 SELENBP1 SELENOP HIST1H4C TFF3 RPS8 RPL23 MT-ND4 FCGBP CEACAM6 FYB1 FCGBP TFF3 LCN2 MT-ATP8 BEST4 LDHB GUCA2A MT-ND3 MYCBP2 BMP7 LAPTM5
5 CA2 CEACAM7 JUN SPINK4 RPL34 RPL35A MT-ND2 GSN ANXA2 HPGDS REP15 WFDC2 LEFTY1 SELENBP1 MT1G H2AFZ CD177 MT-ATP8 S100A4 APCDD1 SLC2A3
6 MT2A GUCA2A HIST1H2BG MUC2 RPL3 RPS12 MT-ATP6 TFF3 PMEPA1 PLCG2 WFDC2 REG4 B3GNT7 MT-ATP6 GUCA2A TUBA1B SELENOP MT-ND1 LYZ RBP1 HLA-DRB1
7 KRT19 PLAC8 IER2 REP15 RPLP0 RPL7 MKI67 TSPAN1 KRT17 PSTPIP2 MUC2 AGR2 DMBT1 MT-ND1 MT1H RPL23 CEACAM7 HLA-DRA TPM2 NOTUM SRGN
8 MT1M ISG15 ZFP36L2 ST6GALNAC1 RPS28 RPS27A ATAD5 CD177 TIMP1 AZGP1 CLCA1 MUC2 NUPR1 SLC26A2 MT2A HSP90AB1 TMIGD1 VIM IFITM1 ARHGDIB
9 MT1G IFI27 PPP1R15A KLK1 RPL5 RPS18 BRCA2 ANKRD36C TM4SF1 COL27A1 KLK1 KLK1 GOLM1 MT-ND4 CA4 RPS7 MS4A12 LGALS1 AC020656.1 TSC22D3
10 CKB TSPAN1 MAFB SERPINA1 LEFTY1 RPS15A LCN15 SYTL2 KLK10 BMX SERPINA1 SPINK1 AGR2 MT-ND5 SPIB PCCA GUCA2B SRGN PTPRO TNFAIP3
11 ADIRF SLC9A3 IER5L HEPACAM2 RPS24 RPL7A CENPJ IFI27 S100P ALOX5 RETNLB FCGBP SLPI MT-ND3 HES4 PSMA7 ABCG2 SYNE2 CLDN2 APOE
12 MT1E MS4A12 BTG1 SPDEF RPSA RPL10 CENPF REP15 LMO7 MARCKSL1 RPL36 ST6GALNAC1 AGR3 MT-ND4L MT1M SET TRPM6 CD74 PCP4 HLA-DRA
13 FXYD3 ANPEP Z93241.1 ANO7 RPL10A FTL MT-CO2 CDC42EP3 SLC2A1 ATP2A3 SPDEF SERPINA1 NXPE4 PLCE1 PCSK1N RPSA SGK1 LMO7 KCNMB4 IL7R
14 LGALS3 CEACAM1 EGR1 RAP1GAP RPL9 RPL19 MT-CO3 SPATS2L LAMC2 ITPR2 ST6GALNAC1 REP15 SULT1B1 MT-CO1 FRMD1 RPL7A ANPEP HLA-DRA SBSPON ZNF331
15 MT1H PHGR1 PPP1R10 ZG16 RPL32 RPS2 NOP56 ENTPD8 TFF2 PTPN18 RAB26 SLC12A2 SPINK5 CA2 NEURL1 RAN ABCB1 MTTP MT-ND3
16 SLC26A3 FABP1 IER5 ATOH1 RPLP2 RPS14 TGFBI SMIM14 ABHD2 CCSER1 ATOH1 XBP1 ADH1C DMBT1 RPL27 SECTM1 CTTNBP2 CD74
17 LGALS4 KRT20 JUNB BEST2 RPS29 RPL32 TOP2A SCNN1A PKM HCK L1TD1 HEPACAM2 SLC28A2 HRCT1 LDHA PLAC8 CYP2W1 CD69
18 MS4A12 HPGD NRARP SLC4A7 RPL6 RPS3A MT-ND3 MGLL TACSTD2 RASSF6 RPS15 RNASE1 NXPE1 SCIN HSPE1 HPGD PLA2G4A CD83
19 MT1X MUC12 AL355075.4 RETNLB RPS2 RPLP1 FN1 MLPH ERO1A MATK RASD1 KIAA1324 TSPAN8 ADRA2A TOP2A LINC02023 CYP4X1 HSPA1A
20 KRT20 SDCBP2 SOCS1 B3GNT6 RPL14 RPS21 MACC1 KLK1 SLC7A11 IL17RB REG4 TSPAN13 RARRES1 CARD16 GAPDH MT-CO1 AC083809.1 NR4A2
21 TMEM54 MISP AL137077.2 MLPH RPS12 RPL5 NAP1L1 PLAC8 ANXA3 TLE4 TPSG1 CREB3L1 SIAE ADCY5 RPL7 CA4 STMN3 HLA-DPA1
22 CEACAM7 EMP1 HIST1H2AG MT-ND1 RPL29 RPL13 HSPD1 RAB27A FOXQ1 IFI6 RAP1GAP FABP2 CFTR CTSE NPM1 MT-CO2 PTP4A3 RGS1
23 KRT8 GUCA2B CSKMT SYTL2 RPL37 RPL6 NCL RASEF ITGA2 PTGS1 SPINK1 RETNLB GPX2 NOTCH2 POMP RARRES3 ELFN1-AS1 NFKBIA
24 ETHE1 CA4 HIST1H2AH WFDC2 RPL23 RPL12 EIF3B TM4SF5 CD46 AVIL RPS11 SPDEF SI SLC2A5 RPS4X SLC17A4 CLU GNAI2
25 PIGR HIST1H1C LINC01970 KIAA1324 MLEC NACA ATRX BCAS1 SERPINB5 GRASP BTG2 CKAP4 TNFRSF11A CDK18 RPL19 ISG15 GAL HSPA1B
26 SLC26A2 FTH1 HSPA1B ERN2 PPP1R1B RPS20 MPHOSPH8 SERPINA1 MSLN SH2D7 JUN C12orf57 CD24 MYOM1 RPS27A MT-ND3 CNTNAP2 HSPH1
27 C10orf99 CD177 BTG2 XBP1 ADH1C RPS6 RPL35 FER1L6 CD55 SPTLC2 RPL13 ATOH1 KLF5 MEIS1 NAP1L1 MT-ND2 DACH1 MZB1
28 BSG PRSS3 AL031777.3 MUC4 C1QBP RPL10A MT-ATP8 QSOX1 TNFRSF12A PBXIP1 RPL28 GMDS FAM3D OTOP3 RPL6 EMP1 BMP4 DNAJB1
29 CDKN2B-AS1 CDHR5 FOSB WNK4 CCND2 RPL24 MT-ND4L TBX10 MET ZFHX3 RPS27 RAP1GAP MAOA C2orf54 PTMA TRIM31 CPNE7 REL
30 UGT2B17 TRIM31 MALAT1 FRYL UGT2A3 RPS23 RNF213 TPSG1 TRIM29 HIP1R RPL18A TPSG1 MUC4 UNC5C RANBP1 MUC12 CXCL1 IER5
31 CHCHD10 PKIB HIST1H3A SPINK1 IMPDH2 RPL27 SOX9 CREB3L1 CTSE B4GALNT4 ZG16 RAB27A RNF186 PRKG2 RPS2 SLC51B TESC KDM6B
32 CES2 FXYD3 IER3 MT-ND2 PTGDR RPL23A KCNQ1OT1 SPDEF TESC ALOX5AP RPL29 L1TD1 AKR1C3 NBPF19 ENO1 CDHR5 CLDN1
33 CDHR5 TMEM54 GADD45B MT-ND3 DUT RPS13 ARGLU1 VIPR1 KRT6B HTR3E RPL18 TCEA3 ARF4 NBPF14 RPL35 TMEM37 SP5
34 TST RHOC CITED2 RNASE1 FBL RPL30 IGLC2 GPR153 AQP5 OGDHL RPL13A ARFGEF3 MECOM SAMD9L NCL TSPAN1 DPYSL2
35 PRSS3 TMIGD1 RASD1 REG4 RPL13A RPL3 TRANK1 PLA2G16 AFAP1L2 RPS18 ANXA13 SPINK1 MT1F ACTG1 SLC9A3 PSMG1
36 LGALS2 GPA33 POU3F1 HPCAL1 RPS23 TPT1 DDX60 FXYD5 HOTAIRM1 KRT18 BEST2 DUOX2 TTC39B GSTP1 MT-ATP6 DMKN
37 HSD11B2 DUOX2 AC023157.3 GNE RPS4X HSP90AB1 DHRS9 DCBLD2 ANXA13 AGR2 AC005833.1 MLEC CDHR2 RPS21 CDA CTSH
38 MT1F TMPRSS2 ID4 L1TD1 NUPR1 RPL8 MINPP1 ECM1 GRK5 RPS9 HPCAL1 MPC2 LYPD8 RPS20 BMP3 DPEP1
39 SLC51B HLA-A CEBPB PRKAG2 TRABD2A RPSA FOXA3 TNFAIP2 GNG13 RPL37 FMOD LIMA1 MT1E DEK PDE9A OLFM4
40 CHP2 CA2 AL118516.1 MT-ND4 RPL22 RPS3 BEST2 PRSS22 ADGRG6 RPL12 ERGIC1 PPP1R1B CEACAM1 RPL23A PDZD3 DMBT1
41 ANPEP MYL12B CDKN1C AGR2 RPLP1 RPS19 B3GNT6 CEMIP SPIB COL16A1 GNE LRIG3 MT1X RPS15A SDCBP2 FZD3
42 PKIB SFN SOCS3 CRACR2B PEBP1 RPL37A RFLNA KLK6 RGS13 RPS19 MYADM MGST2 SDCBP2 RPL5 PKIB MYC
43 PLAC8 MDK POLR2A MT-CO3 RPS19 RPS5 SMIM5 IGFBP3 TAS1R3 XBP1 MLPH TXN KRT20 SNRPF HIST1H1C GNG4
44 C2orf88 MUC13 HIST1H2BF RASD1 RPS27A EEF1B2 SMIM6 BMP4 POU2F3 RPS24 FOXA3 KCNN4 MSLN HMGA1 C2orf88 RPS4Y1
45 DHRS11 SGK1 AMD1 GALNT5 ATP5MC1 RPL37 ATOH1 CDKN2A KIT RPL14 ALDH1A1 ATP8B1 GNPTAB TUBB CDHR2 ASCL2
46 SULT1B1 CLDN4 AC005837.1 AKAP9 RPL11 BTF3 CAPN9 TGM2 DKK3 FOSB B3GNT6 UGT2A3 HEPACAM2 BTF3 MEP1A CXCL2
47 AKR1B10 SLC51B AC091271.1 NEDD4L RPS18 RPL9 RAB3B COL6A1 TUBA1A RPS8 NUCB2 RHBDL2 CKB RPL24 SMPDL3A FAM84B
48 GUCA2A ATP1B3 AL021453.1 MT-ATP8 FABP5 RPL11 SYTL5 CXCL16 CD300LF CRACR2B SLC4A7 PPP1R12B VIPR1 RPL35A MIR194-2HG LYZ
49 GPT TNFSF10 H3F3B HSD11B2 RPL37A RPL35 LGALS9B CLIC3 DPYSL3 JUNB DNAJC12 SQOR GUCY2C LCN15 C11orf86 FAM210B
50 C1QTNF12 NEAT1 RHOB GOLGB1 SUCLG1 RPS24 IL3RA AHNAK2 SLCO3A1 NR4A1 DLL1 CES2 ECE1 CHCHD2 MT-ND4L ZNRF3
51 ACADS CEACAM6 HIST1H4E IGKC EEF1B2 RPS16 FAM177B VNN1 TREH RPS12 SELENOM PRAC1 AOC1 NACA FABP1 CNOT7
52 ATP5F1D PRDX6 DNAJB1 JCHAIN NUCKS1 RPL34 SYT7 RAMP1 PIK3CG RPL32 MB APP CEACAM7 YBX1 GPA33 GRINA
53 BLOC1S1 PLS1 DDIT4 RPL23A RPS8 SAMD9 DUSP4 VAV1 RPL35 FRZB MUC12 MALT1 RPL8 RHOU TGFBR3
54 AHCYL2 FCGRT CYBA RPL18A GAPDH CLDN8 NECTIN4 DCLK2 CDC42EP5 ANO7 HOXB13 GPA33 PTTG1 CDKN2B-AS1 LACTB2
55 UQCRQ UGP2 MED29 RPS14 COMMD6 GPRIN2 KRT80 HTR3C RPLP1 GALNT8 NFIB CDHR5 PSMB1 SULT1A2 CPNE1
56 S100A6 CDA HIST1H1E TXN NPM1 FAM3D PDLIM7 KCNQ4 ERN2 TMEM61 CLINT1 PROX1 RPLP0 SAMD9 BACE2
57 FLNB C11orf86 HIST1H2BH EIF3L EIF3E NAAA BST2 NCMAP MUC4 SMAD9 MUC5B CLCA4 RPS3 MT-ND1 TM4SF1
58 COX5B TMEM37 RPS19 CD99 RPLP0 MFSD4A KLK11 FRY IER5 CAPN9 PAPSS2 SAMD9 PTGES3 MISP MLXIPL
59 SULT1A1 CLDN3 TCIM RPS16 RPL31 MUC13 FSTL3 PLCB2 RPL27A RAB15 GALNT1 C1orf21 PTMS SCNN1B NFE2L3
60 PLCD3 ITM2C PMAIP1 RPL4 RPL4 DST LAMB3 CGNL1 IER2 CREB3L4 FAM162A EEF2K RPL32 MDK IFITM3
61 SLC9A3 HLA-C KCNQ1OT1 SLC25A6 RACK1 VSIG2 CAPG PAK3 ANO7 ZG16 S100A11 SRI PRDX1 HHLA2 NCOA7
62 ELOB VAMP8 CBX4 RPS13 RPLP2 MLLT3 LAMA3 LUC7L3 RPL37A SMIM14 C15orf48 SLC20A1 PRKDC NAAA CASP1
63 SLC4A4 SMPDL3A SRSF7 RPL8 RPS28 SELENOP PON2 PLEKHB1 RPS2 SCGB2A1 PKP2 TMEM176A EEF1B2 MXI1 AHCY
64 AMN SAMD9 ELF3 OLFM4 RPL13A SCGB2A1 S100A4 TBC1D2B BEST2 RAB26 PLCB4 PDE9A RPS6 AAK1 PLTP
65 TP53I3 SPATS2L ZFP36 GMNN HSPD1 ISG20 CTSH EIF1B SH3BGRL3 SLC9A3R2 TSPO CFD RPS12 CYP3A5 DEPTOR
66 TPRN PRSS8 HSPA1A RPS21 RPS10 FXYD3 TFF1 MTSS1 RNASE1 TSTA3 TFCP2L1 TMEM176B SLC25A5 MT-ND5 CSE1L
67 SFN MEP1A ARGLU1 RPS5 S100A11 SLC16A9 ANXA1 TPM1 RPS29 RPS11 TM9SF3 GSN RPS13 APPL2 CD81
68 MAOA CLDN23 SELENBP1 RPL12 PSMA7 EIF2AK3 PITX1 PTPRJ EGR1 RPL10 ATP5F1A LINC01559 RPS3A MIER3 NR2F1
69 CD24 SMIM22 HSP90AA1 ATP5MC2 PPA1 P2RX4 S100A16 BCAM RPL8 RPS12 CYBA HSD17B2 RPL4 TXNIP NFIA
70 PAPSS2 HSD17B2 FOS APEX1 RPL27A HEPACAM2 BACE2 IGSF3 RPS5 KDELR1 PGM2L1 SLC17A4 PPA1 IFI27 ZFAS1
71 MVP DST ID2 RPS7 RPL18A MCF2L GPRC5A KRT18 TCIM RPL36 PTP4A1 PHGR1 CENPF PHGR1 TNFRSF12A
72 MYL6 SERINC2 RPL13 RPL19 RPS27 HLA-E MACC1 UTRN RPL11 RPLP1 PLCE1 DSC2 RPS18 RHOC SCCPDH
73 NDUFA1 DHRS9 YME1L1 RPL35 ZFAS1 LPIN2 TGFBI JCHAIN RPS16 FAM3D CCL28 TP53INP1 PCNA MT-CO3 APEX1
74 SMIM22 SRI HSPA2 RPL7 RPL28 TUBB2A HMGA1 JMY HPCAL1 RPL34 PRKACB TMSB10 IFITM3 SMCHD1 TACSTD2
75 MISP CDHR2 CEBPD HMGCS2 RPL38 FAM107B PPA1 LIMCH1 SOX4 AGR3 MGST3 MDK TPI1 C1QTNF12 PABPC1
76 CHP1 CFDP1 SFPQ RPL24 RPL14 MUC4 BCL2L1 CHD6 RPS14 SH3BGRL3 CTSS PTPRR SNRPG TNFSF10 GLO1
77 ID1 ASS1 PNN PHB2 RPS11 GDPD3 GSTP1 PTPN6 MLPH AQP3 SRI VSIR RPS23 DST ZFAND1
78 NDUFB7 CGN VEGFA PRDX3 ACTG1 FSIP2 FIBCD1 ARHGEF38 HSPA1A PLXDC2 ANXA2 FABP1 RPL37A CFDP1 C2CD4A
79 ITM2C C2orf88 SRRM2 RPS11 RPL29 LINC01559 LYZ MAP7 SLC4A7 ARF4 TCEA3 MEP1A HSP90AA1 MXD1 MRPL15
80 GIPC1 RARRES3 RPS18 RPL13 RPL18 MAN1A1 POMP FURIN RPL30 RPL27A TC2N ITM2C HSPA8 ENTPD8 EIF6
81 VSIG2 CLTB RPL35 UQCRH GSTP1 SECTM1 SLPI SELENOM ELF3 B4GALNT2 S100A10 TP53INP2 ATP5MC1 MT-ND4 EPHB2
82 AOC1 MXI1 RPS15 RPS15A POMP CCDC68 C4BPB IGKC RPL19 GALNT12 SUCLG1 PRR5L SSB CDKN2B TNFRSF10B
83 ATP5ME GPRC5A HNRNPU RPL18 RPL36 PARM1 TINAGL1 LIPG RPL10 FKBP11 HSPA1A CEACAM6 RPS14 CCDC68 PDP1
84 GGT6 SECTM1 SNHG8 RPL27A NDUFA4 TP53INP1 DUOXA2 KMT2C RPL35A IL13RA1 PPA1 TDP2 BIRC5 CEACAM1 FITM2
85 SRI CDKN2B-AS1 SLC38A2 RPL31 RPS9 GALNT5 DNAJC15 PGGHG TSTA3 CDC42EP5 HIF1A FXYD3 GPX2 FXYD3 CXCL3
86 UQCR11 RFK PCK1 RPS9 YBX1 WNK4 HEBP2 CAPN12 KIAA1324 HES6 PDZK1IP1 A1CF TPX2 PRSS3 DPM1
87 PRDX6 DSC2 RPL28 ESD HSPE1 NEDD4L GTF3A ARGLU1 RPL10A FOXP1 FAM120A HSD17B11 PERP CTSA EIF3E
88 AKR1C3 EFHD2 DUSP1 RPL7A ATP5F1E HLA-A S100A2 MALAT1 RPS15A IGFBP2 NFKBIZ NSD2 SERBP1 SLC6A8 MIF
89 PPDPF ACAA2 BRD2 YBX1 CHCHD2 SDCBP2 PRDX1 FGFR4 RPL7A RPL3 PI3 CA2 CCT5 CGN SNHG15
90 UQCRC1 MYL6 C6orf62 RPS27 RPL39 TCF7L2 SCD IL13RA1 RPL3 NEDD4L UQCRC2 S100A10 C1QBP SERINC2 HIBADH
91 ATP5MD RHOF RND3 RPS20 CLIC1 HLA-F YAP1 ANXA1 HSPA1B PRUNE2 ADD3 FNIP2 CCT7 HLA-A DUSP4
92 S100A10 PDE9A NFKBIA LBR RPS15 HLA-C LCN2 CD14 RPL38 NEURL1 HINT1 FLNB PDIA6 COL17A1 SINHCAF
93 MRPL41 LGALS3 PRAC1 LDHB KRT20 UCHL3 CCDC88B SSR4 GALNT7 LGALS3 APOBR CCT2 SLC9A3R1 AGPAT5
94 COX7B CTSA ATP5PB SET PHGR1 TPM4 MYO1B FOS LMAN1 LGALS2 MISP RPL3 TCF7L2 MFHAS1
95 PRR13 SLC6A8 MRPL11 HINT1 TPM1 AKAP12 BTG2 KLF4 RASD1 NANS KRT8 IGFBP2 TMPRSS2 FDFT1
96 COX6B1 CTSZ NACA PTMA S100P CCND1 TET2 CREB3L1 NANS LAPTM4A CDC42BPA GGCT LIPH VWA1
97 CHMP2A SLC17A4 RPL39 NAP1L1 PLA2G10 CXCL8 DEFB1 RPLP0 KLF4 PYCARD ID1 EIF3E PDCD4 LYPLA1
98 S100A14 UPP1 ATP5F1A FAU RARRES3 PHLDA2 PPDPF HEPACAM2 GLUL ATP5PB C10orf99 GGH ATP1B3 TGFBI
99 ATP5PF PI3 CDCA7 EIF3H LIPH FLNA BIK IER3 LGALS4 GPR160 MT-CO1 RPS10 RFK CPNE3
100 MT-ND5 MYL12A CFTR PRDX1 DYRK2 S100A13 H1FX RPS23 RPS3A SCP2 CHP2 NDUFA4 FCGRT C1QBP